You can download sopdf from the link I gave above -- but it won't remove the notes.
Your best bet is to go back to using calibre for the conversions if the conversion worked well otherwise. There's an option in calibre to use a RegEx expression to remove headers and footers, and it could be used to remove this note too.
See here:
http://calibre-ebook.com/user_manual...rs-and-footers
If you have trouble making it work, try asking in the calibre forum.